Filter BAM file for mapped reads only

To get only the mapped reads use the parameter 'F', which works like -v of grep and skips the alignments for a specific flag.

samtools view -b -F 4 file.bam > mapped.bam

To get the unmapped reads from a bam file use :

samtools view -f 4 file.bam > unmapped.sam 

the output will be in sam.

to get the output in bam use : 

samtools view -b -f 4 file.bam > unmapped.bam

From the manual; there are different int codes you can use with the parameter 'f', based on what you want :

-f INT Only output alignments with all bits in INT present in the FLAG field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]

Each bit in the FLAG field is defined as:

Flag        Chr     Description
0x0001      p       the read is paired in sequencing
0x0002      P       the read is mapped in a proper pair
0x0004      u       the query sequence itself is unmapped
0x0008      U       the mate is unmapped
0x0010      r       strand of the query (1 for reverse)
0x0020      R       strand of the mate
0x0040      1       the read is the first read in a pair
0x0080      2       the read is the second read in a pair
0x0100      s       the alignment is not primary
0x0200      f       the read fails platform/vendor quality checks
0x0400      d       the read is either a PCR or an optical duplicate

Like for getting the unique reads (a single read mapping at one best position); I use :

-q INT Skip alignments with MAPQ smaller than INT [0]

samtools view -bq 1 file.bam > unique.bam